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Commits on Jun 18, 2015

• merge dev again ???

  brentp

  committed
  68ae163

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• Merge pull request #482 from brentp/inheritance-revamp

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  arq5x

  committed
  1f9eb2c

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• handle repeated columns when requested in query. see #479

  brentp

  committed
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Commits on Jun 17, 2015

• Merge pull request #480 from brentp/inheritance-revamp

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  arq5x

  committed
  8bc4c68

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• add test for phasing

  brentp

  committed
  0a07990

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• test and improve backwards compat (dbs without GL columns)

  brentp

  committed
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• update tests related to mendelian error tool.

  brentp

  committed
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Commits on Jun 16, 2015

• working mendelian errors

  brentp

  committed
  3ef1825

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• comphets has phase-by-transmission as default

  brentp

  committed
  a81c02b

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• update auto_dom tests

  brentp

  committed
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Commits on Jun 15, 2015

• update tools to default to requiring affected_only (opposite flag is --allow-unaffected)

  brentp

  committed
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Commits on Jun 12, 2015

• more small changes with new family setup

  brentp

  committed
  770c322

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• update more tests to new setup

  brentp

  committed
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Commits on Jun 4, 2015

• update auto_rec tests

  brentp

  committed
  2ec209e

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• update tests for comphet

  brentp

  committed
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Commits on May 21, 2015

• handle --no-genotypes argument as reported on mailing list

  brentp

  committed
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Commits on May 18, 2015

• handle sample names with dashes and handle case-issues -- as reported by Uma

  brentp

  committed
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Commits on May 13, 2015

• some cleanups

  brentp

  committed
  39fda9e

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• more tests for bcolz

  brentp

  committed
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Commits on May 12, 2015

• more tests for bcolz.

  brentp

  committed
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• index gt columns with bcolz on load by default.

  brentp

  committed
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Commits on May 4, 2015

• incorporate changes from #453

  brentp

  committed
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• more edge-cases for bcolz.

  brentp

  committed
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• working bcolz

  brentp

  committed
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• update tests

  brentp

  committed
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Commits on Apr 22, 2015

• add tests for mendelian error

  brentp

  committed
  d510e2b

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• update comphet tests

  brentp

  committed
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• update de-novo tests for new format

  brentp

  committed
  580bf7d

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• update auto-rec tests for new format

  brentp

  committed
  b928c03

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• update auto-dom tests for new format

  brentp

  committed
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• bed output for stuff from inheritance factory

  brentp

  committed
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Commits on Apr 6, 2015

• Merge pull request #429 from brentp/genotype-likelihoods

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  arq5x

  committed
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• add more tests and document changes to database schema

  brentp

  committed
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• split likelihoods to homref, het, homalt cols

  brentp

  committed
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Commits on Apr 2, 2015

• tests and impl of GLs

  brentp

  committed
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